RetrogeneDB ID: | retro_mmus_1472 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 16:62601876..62602476(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Nsa2 | ||
| Ensembl ID: | ENSMUSG00000060739 | ||
| Aliases: | Nsa2, 5730427N09Rik, LNR42, Nsa2p, Tinp1, Yr29 | ||
| Description: | NSA2 ribosome biogenesis homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1913883] |
Retrocopy-Parental alignment summary:
>retro_mmus_1472
GAAAATACAATTAAGATGTATGGAAAGAGAAACACGAAGCAGAAGGATGATGAGAAGACTCCACAGGGAGCGTCCCCACC
TATCTGCTGGACAGAGAGGGGCAGTTGAGAGCAAAAGTACTTTCCAACATGATTAAGCAGAAACGAAAAGAAAAGGCAGG
AAAATGGGAGGTCCCTCTATGCATAGTTCGTGTCTAAGGAGAAACAGAACTATTGAAAGTTATTTGAACAGGGAGAAATA
AAAAAAAGAAGGCATGGAAGAGAATGGTTACTAAAGTCTGCTCTGTTGGCGATGGCTTTACAAGAAAACCACCTAAATAT
GAAAGATTCATTAGGTCAATGGGTCTACGTTTCATAAAAGCCCATGTCACACACAGGAGCTGAAAGCTACCTTTTGCCTG
CCTATATACTGTGTGAAAAAGAATCCACCATCCCCATTATATACAAATATACAATCCTGGGTGTGATCACCAAAGGTACA
GTTCCTGAAGTGAATGTGAGCGAGTTGGACCTTGTAACACAAGGAGGCTAGGTGATTTGGAGAGTGTATGCCCAAGTTAC
CAACAATCCTGAAAACGATGGGTGCATCAATGCTGGTCTT
ORF - retro_mmus_1472 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 79.9 % |
| Parental protein coverage: | 75.77 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | KKTIKMHEKRNTKQKDDEKTPQGA-VPAYLLDREGQSRAKVLSNMIKQKRKEKAGKWEVPLPKVRAQGET |
| ..TIKM..KRNTKQKDDEKTPQGA.VP.YLLDREGQ.RAKVLSNMIKQKRKEKAGKWEVPL..VR..GET | |
| Retrocopy | ENTIKMYGKRNTKQKDDEKTPQGA<VPTYLLDREGQLRAKVLSNMIKQKRKEKAGKWEVPLCIVRV*GET |
| Parental | EVLKVIRTGKRKK-KAWKRMVTKVCFVGDGFTRKPPKYERFIRPMGLRFKKAHVTH-PELKATFCLPILG |
| E.LKVI.TG.....KAWKRMVTKVC.VGDGFTRKPPKYERFIR.MGLRF.KAHVTH..ELKATFCLPI.. | |
| Retrocopy | ELLKVI*TGRNXXXKAWKRMVTKVCSVGDGFTRKPPKYERFIRSMGLRFIKAHVTH<QELKATFCLPIYC |
| Parental | VK-KNPSSPL---YTTLGVITKGTVIEVNVSELGLVTQGGKVIWGKYAQVTNNPENDGCINAVL |
| VK.K....P....YT.LGVITKGTV.EVNVSEL.LVTQGG.VIW..YAQVTNNPENDGCINA.L | |
| Retrocopy | VK<KESTIPIIYKYTILGVITKGTVPEVNVSELDLVTQGG*VIWRVYAQVTNNPENDGCINAGL |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| SRP007412_brain | 0 .00 RPM | 10 .05 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 9 .99 RPM |
| SRP007412_heart | 0 .00 RPM | 16 .09 RPM |
| SRP007412_kidney | 0 .00 RPM | 22 .87 RPM |
| SRP007412_liver | 0 .00 RPM | 19 .72 RPM |
| SRP007412_testis | 0 .00 RPM | 25 .52 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1472 was not detected
No EST(s) were mapped for retro_mmus_1472 retrocopy.
No TSS is located nearby retro_mmus_1472 retrocopy 5' end.
retro_mmus_1472 was not experimentally validated.